Difference between revisions of "BamUtil: dumpRefInfo"

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= Overview of the <code>dumpRefInfo</code> function of <code>bamUtil</code> =
 
= Overview of the <code>dumpRefInfo</code> function of <code>bamUtil</code> =
 
The <code>dumpRefInfo</code> option on the [[bamUtil]] executable prints the SAM/BAM file's reference information.
 
The <code>dumpRefInfo</code> option on the [[bamUtil]] executable prints the SAM/BAM file's reference information.
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= Usage =
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./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs] [--params]
  
 
= Parameters =
 
= Parameters =
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         --params          : print the parameter settings
 
         --params          : print the parameter settings
 
</pre>
 
</pre>
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{{PhoneHomeParamDesc}}
  
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== Required Parameters ==
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{{InBAMInputFile}}
  
printRecordRefs outputs the id, the name, and the number of records with that id/name in the SAM/BAM file.  
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== Optional Parameters ==
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{{noeofBGZFParameter}}
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=== Print Number of Records for each Chromosome (<code>--printRecordRefs</code>) ===
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Use the <code>--printRecordRefs</code> option to also output each reference/chromsome id, name, and the number of records with that id/name in the SAM/BAM file.  
 
Example:
 
Example:
 
<pre>
 
<pre>
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Ref ID: -1 indicates unmapped (Ref Name will be *)
 
Ref ID: -1 indicates unmapped (Ref Name will be *)
  
= Usage =
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{{paramsParameter}}
./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs] [--params]
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{{PhoneHomeParameters}}
  
 
= Return Value =
 
= Return Value =

Latest revision as of 16:54, 6 January 2014


Overview of the dumpRefInfo function of bamUtil

The dumpRefInfo option on the bamUtil executable prints the SAM/BAM file's reference information.

Usage

./bam dumpRefInfo --in <inputFilename> [--noeof] [--printRecordRefs] [--params]

Parameters

    Required Parameters:
        --in               : the SAM/BAM file to be read
    Optional Parameters:
        --noeof            : do not expect an EOF block on a bam file.
        --printRecordRefs  : print the reference information for the records in the file (grouped by reference).
        --params           : print the parameter settings
	PhoneHome:
		--noPhoneHome       : disable PhoneHome (default enabled)
		--phoneHomeThinning : adjust the PhoneHome thinning parameter (default 50)

Required Parameters

Input File (--in)

Use --in followed by your file name to specify the SAM/BAM input file.

The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user, unless your input file is stdin.

A - is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).

SAM/BAM/Uncompressed BAM from file --in yourFileName
SAM from stdin --in -
BAM from stdin --in -.bam
Uncompressed BAM from stdin --in -.ubam


Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the samtools implementation so pipes between our tools and samtools are supported.

Optional Parameters

Do not require BGZF EOF block (--noeof)

Use --noeof if you do not expect a trailing eof block in your bgzf file.

By default, the trailing empty block is expected and checked for.

Print Number of Records for each Chromosome (--printRecordRefs)

Use the --printRecordRefs option to also output each reference/chromsome id, name, and the number of records with that id/name in the SAM/BAM file. Example:

	Ref ID: 0	Ref Name: 1	NumRecs: 4

Ref ID: -1 indicates unmapped (Ref Name will be *)

Print the Program Parameters (--params)

Use --params to print the parameters for your program to stderr.

PhoneHome Parameters

See PhoneHome for more information on how PhoneHome works and what it does.

Turn off PhoneHome (--noPhoneHome)

Use the --noPhoneHome option to completely disable PhoneHome. PhoneHome is enabled by default based on the thinning parameter.

Adjust the Frequency of PhoneHome (--phoneHomeThinning)

Use --phoneHomeThinning to modify the percentage of the time that PhoneHome will run (0-100).

  • By default, --phoneHomeThinning is set to 50, running 50% of the time.
  • PhoneHome will only occur if the run's random number modulo 100 is less than the --phoneHomeThinning value.
  • N/A if --noPhoneHome is set.

Return Value

  • 0: the file was processed successfully.
  • non-0: the file was not processed successfully.

Sample Output

Reference Index 0; Name: 1
Reference Index 1; Name: 2
Reference Index 2; Name: 3
Reference Index 3; Name: 4
Reference Index 4; Name: 5
Reference Index 5; Name: 6
Reference Index 6; Name: 7
Reference Index 7; Name: 8
Reference Index 8; Name: 9
Reference Index 9; Name: 10
Reference Index 10; Name: 11
Reference Index 11; Name: 12
Reference Index 12; Name: 13
Reference Index 13; Name: 14
Reference Index 14; Name: 15
Reference Index 15; Name: 16
Reference Index 16; Name: 17
Reference Index 17; Name: 18
Reference Index 18; Name: 19
Reference Index 19; Name: 20
Reference Index 20; Name: 21
Reference Index 21; Name: 22
Reference Index 22; Name: X
	Ref ID: 0	Ref Name: 1	NumRecs: 4
	Ref ID: 1	Ref Name: 2	NumRecs: 1
	Ref ID: 0	Ref Name: 1	NumRecs: 1
	Ref ID: 1	Ref Name: 2	NumRecs: 1
	Ref ID: 2	Ref Name: 3	NumRecs: 1
	Ref ID: -1	Ref Name: *	NumRecs: 2